Loading report..

Highlight Samples

This report has flat image plots that won't be highlighted.
See the documentation for help.

Regex mode off

    Rename Samples

    This report has flat image plots that won't be renamed.
    See the documentation for help.

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      This report has flat image plots that won't be hidden.
      See the documentation for help.

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Save Settings

        You can save the toolbox settings for this report to the browser.


        Load Settings

        Choose a saved report profile from the dropdown box below:

        About MultiQC

        This report was generated using MultiQC, version 1.9

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2020-07-31, 11:40 based on data in: /tmp/tmpbsuve6dm


        General Statistics

        Showing 234/234 rows and 6/10 columns.
        Sample NameM Reads Mapped% AlignedInsert SizeMedian CoverageBases ≥ 20XBases ≥ 30X
        LKCGP-P000201-244412-01-06-01-R1
        120.0X
        98%
        98%
        LKCGP-P000201-244412-01-06-01-R1.H3NTMCCXY-L6
        938.6
        LKCGP-P000201-244412-01-06-01-R1.H3NTMCCXY-L7
        930.4
        LKCGP-P000201-244412-01-06-01-R1.H3NTMCCXY-L8
        984.1
        LKCGP-P000201-244413-01-06-07-G1
        976.6
        42.0X
        95%
        89%
        LKCGP-P000601-245664-01-06-01-D1
        108.0X
        97%
        97%
        LKCGP-P000601-245664-01-06-01-D1.H3LHGCCXY-L3
        918.9
        LKCGP-P000601-245664-01-06-01-D1.H3LHGCCXY-L4
        895.3
        LKCGP-P000601-245664-01-06-01-D1.H3LHGCCXY-L5
        922.8
        LKCGP-P000601-245666-02-06-07-G1
        920.6
        38.0X
        96%
        86%
        LKCGP-P000803-262693-01-02-09-G2
        934.8
        34.0X
        96%
        77%
        LKCGP-P000803-283756-01-02-03-R2
        103.0X
        98%
        98%
        LKCGP-P000803-283756-01-02-03-R2.HYNGWCCXY-L3
        914.8
        LKCGP-P000803-283756-01-02-03-R2.HYNGWCCXY-L4
        939.0
        LKCGP-P000803-283756-01-02-03-R2.HYNGWCCXY-L5
        924.3
        LKCGP-P000803-285371-01-02-03-G3
        776.0
        28.0X
        77%
        46%
        LKCGP-P000806-246359-02-04-07-G1
        963.2
        40.0X
        97%
        90%
        LKCGP-P000806-246360-01-04-01-D1
        105.0X
        98%
        97%
        LKCGP-P000806-246360-01-04-01-D1.H7JMJCCXY-L3
        951.8
        LKCGP-P000806-246360-01-04-01-D1.H7JMJCCXY-L4
        956.2
        LKCGP-P000806-246360-01-04-01-D1.H7JMJCCXY-L5
        948.4
        LKCGP-P000808-277069-01-02-01-G2
        900.7
        36.0X
        96%
        83%
        LKCGP-P000808-277070-01-02-03-R2
        108.0X
        98%
        97%
        LKCGP-P000808-277070-01-02-03-R2.HYGLNCCXY-L5
        925.7
        LKCGP-P000808-277070-01-02-03-R2.HYGLNCCXY-L6
        914.9
        LKCGP-P000808-277070-01-02-03-R2.HYGLNCCXY-L7
        907.3
        LKCGP-P000808-279684-01-02-08-G3
        939.8
        37.0X
        94%
        81%
        LKCGP-P001103-270604-01-02-03-R1
        104.0X
        98%
        98%
        LKCGP-P001103-271125-01-02-01-G2
        36.0X
        96%
        84%
        LKCGP-P001502-259175-02-01-07-G1
        928.0
        38.0X
        94%
        84%
        LKCGP-P001502-260042-01-01-01-R1
        103.0X
        98%
        98%
        LKCGP-P001502-260042-01-01-01-R1.HH355CCXY-L4
        939.1
        LKCGP-P001502-260042-01-01-01-R1.HH355CCXY-L5
        886.6
        LKCGP-P001502-260042-01-01-01-R1.HH355CCXY-L6
        863.1
        LKCGP-P001805-283771-01-01-01-D1
        111.0X
        98%
        98%
        LKCGP-P001805-283771-01-01-01-D1.H2VYCCCX2-L5
        899.2
        LKCGP-P001805-283771-01-01-01-D1.H2VYCCCX2-L6
        955.2
        LKCGP-P001805-283771-01-01-01-D1.H2VYCCCX2-L7
        881.9
        LKCGP-P001805-283773-02-01-07-G1
        934.7
        37.0X
        94%
        82%
        LKCGP-P001905-285206-01-02-05-R1
        113.0X
        98%
        98%
        LKCGP-P001905-285206-01-02-05-R1.HYNH2CCXY-L4
        951.7
        LKCGP-P001905-285206-01-02-05-R1.HYNH2CCXY-L6
        962.5
        LKCGP-P001905-285206-01-02-05-R1.HYNH2CCXY-L7
        953.2
        LKCGP-P001905-285611-01-02-03-G1
        926.5
        36.0X
        93%
        79%
        LKCGP-P002006-260310-01-02-01-G2
        747.9
        30.0X
        89%
        54%
        LKCGP-P002006-260311-01-02-05-R1
        97.0X
        98%
        98%
        LKCGP-P002006-260311-01-02-05-R1.HL2G5CCXY-L4
        813.6
        LKCGP-P002006-260311-01-02-05-R1.HL2GNCCXY-L5
        869.9
        LKCGP-P002006-260311-01-02-05-R1.HL2N2CCXY-L7
        753.2
        LKCGP-P002102-262924-01-04-01-D1
        105.0X
        98%
        97%
        LKCGP-P002102-262924-01-04-01-D1.HL225CCXY-L2
        861.9
        LKCGP-P002102-262924-01-04-01-D1.HL225CCXY-L3
        880.1
        LKCGP-P002102-262924-01-04-01-D1.HL225CCXY-L4
        864.6
        LKCGP-P002102-262981-02-04-07-G1
        846.1
        34.0X
        96%
        74%
        LKCGP-P002207-283109-01-03-01-R1
        101.0X
        98%
        97%
        LKCGP-P002207-283109-01-03-01-R1.H2VY3CCX2-L3
        894.3
        LKCGP-P002207-283109-01-03-01-R1.H2VY3CCX2-L4
        953.4
        LKCGP-P002207-283109-01-03-01-R1.H2VY3CCX2-L5
        892.5
        LKCGP-P002207-284471-02-03-07-G1
        901.4
        35.0X
        96%
        79%
        LKCGP-P002301-257587-01-04-01-D1
        95.0X
        98%
        98%
        LKCGP-P002301-257587-01-04-01-D1.HH57HCCXY-L5
        814.4
        LKCGP-P002301-257587-01-04-01-D1.HH57HCCXY-L6
        783.9
        LKCGP-P002301-257587-01-04-01-D1.HH57HCCXY-L7
        751.7
        LKCGP-P002301-257608-02-04-07-G1
        757.3
        30.0X
        89%
        54%
        LKCGP-P002307-284734-02-03-07-G1
        1005.5
        38.0X
        97%
        88%
        LKCGP-P002307-284737-01-03-01-R1
        105.0X
        98%
        97%
        LKCGP-P002307-284737-01-03-01-R1.H3G7MCCX2-L1
        990.6
        LKCGP-P002307-284737-01-03-01-R1.H3G7MCCX2-L2
        983.4
        LKCGP-P002307-284737-01-03-01-R1.H3G7MCCX2-L7
        989.7
        LKCGP-P002601-237394-01-04-07-G1
        976.3
        40.0X
        96%
        89%
        LKCGP-P002601-260323-01-04-01-P2
        89.0X
        97%
        97%
        LKCGP-P002601-260323-01-04-01-P2.HH3HWCCXY-L3
        733.4
        LKCGP-P002601-260323-01-04-01-P2.HH3HWCCXY-L4
        760.5
        LKCGP-P002601-260323-01-04-01-P2.HH3HWCCXY-L5
        729.4
        LKCGP-P002704-273227-02-04-07-G1
        934.6
        37.0X
        96%
        85%
        LKCGP-P002704-273230-01-04-01-R2
        111.0X
        98%
        97%
        LKCGP-P002704-273230-01-04-01-R2.HVY32CCXY-L6
        963.2
        LKCGP-P002704-273230-01-04-01-R2.HVY32CCXY-L7
        934.7
        LKCGP-P002704-273230-01-04-01-R2.HVY32CCXY-L8
        958.4
        LKCGP-P002805-297243-01-01-01-R1
        102.0X
        98%
        98%
        LKCGP-P002805-297243-01-01-01-R1.H5J2YCCX2-L6
        1016.1
        LKCGP-P002805-297243-01-01-01-R1.H5J2YCCX2-L7
        968.9
        LKCGP-P002805-297243-01-01-01-R1.H5J2YCCX2-L8
        968.8
        LKCGP-P002805-297245-02-01-07-G1
        999.4
        36.0X
        93%
        80%
        LKCGP-P002902-272974-01-02-03-G2
        879.7
        34.0X
        93%
        74%
        LKCGP-P002902-272975-01-02-03-G3
        859.4
        33.0X
        95%
        71%
        LKCGP-P002902-273015-01-02-03-P1
        103.0X
        98%
        98%
        LKCGP-P002902-273015-01-02-03-P1.HYGT7CCXY-L1
        861.6
        LKCGP-P002902-273015-01-02-03-P1.HYGT7CCXY-L2
        913.7
        LKCGP-P002902-273015-01-02-03-P1.HYGT7CCXY-L3
        856.9
        LKCGP-P003001-262014-02-03-07-G1
        775.9
        31.0X
        91%
        61%
        LKCGP-P003001-262058-01-03-01-P1
        86.0X
        98%
        97%
        LKCGP-P003001-262058-01-03-01-P1.HLL53CCXY-L5
        730.3
        LKCGP-P003001-262058-01-03-01-P1.HN7G7CCXY-L1
        759.6
        LKCGP-P003001-262058-01-03-01-P1.HN7G7CCXY-L2
        772.2
        LKCGP-P003307-294721-01-02-05-D1
        121.0X
        98%
        97%
        LKCGP-P003307-294721-01-02-05-D1.H5JLHCCX2-L2
        1006.3
        LKCGP-P003307-294721-01-02-05-D1.H5JLHCCX2-L3
        1007.1
        LKCGP-P003307-294721-01-02-05-D1.H5JLHCCX2-L4
        1021.0
        LKCGP-P003307-297693-01-02-12-G1
        994.4
        39.0X
        95%
        86%
        LKCGP-P003506-274439-01-02-05-G2
        920.9
        36.0X
        96%
        83%
        LKCGP-P003506-274440-01-02-05-G3
        952.9
        36.0X
        94%
        80%
        LKCGP-P003506-274441-01-02-05-R1
        109.0X
        98%
        97%
        LKCGP-P003506-274441-01-02-05-R1.HVY2TCCXY-L3
        906.5
        LKCGP-P003506-274441-01-02-05-R1.HVY2TCCXY-L4
        952.2
        LKCGP-P003506-274441-01-02-05-R1.HVY2TCCXY-L5
        939.2
        LKCGP-P003607-299930-01-01-01-R1
        114.0X
        98%
        97%
        LKCGP-P003607-299930-01-01-01-R1.H7CLLCCX2-L3
        1034.6
        LKCGP-P003607-299930-01-01-01-R1.H7CLLCCX2-L6
        1036.4
        LKCGP-P003607-299930-01-01-01-R1.H7CLLCCX2-L7
        957.2
        LKCGP-P003607-299932-02-01-07-G1
        1017.2
        38.0X
        97%
        87%
        LKCGP-P003804-277725-01-04-01-R1
        102.0X
        98%
        98%
        LKCGP-P003804-277725-01-04-01-R1.HYGNLCCXY-L6
        948.7
        LKCGP-P003804-277725-01-04-01-R1.HYGNLCCXY-L7
        930.1
        LKCGP-P003804-277725-01-04-01-R1.HYGNLCCXY-L8
        961.3
        LKCGP-P003804-277728-02-04-07-G1
        945.4
        37.0X
        94%
        81%
        LKCGP-P004301-270831-01-01-01-D1
        107.0X
        98%
        98%
        LKCGP-P004301-270831-01-01-01-D1.HVYJTCCXY-L5
        925.6
        LKCGP-P004301-270831-01-01-01-D1.HVYJTCCXY-L6
        923.8
        LKCGP-P004301-270831-01-01-01-D1.HVYJTCCXY-L7
        894.7
        LKCGP-P004301-270834-02-01-07-G1
        961.1
        36.0X
        94%
        81%
        LKCGP-P004801-275422-01-01-09-G1
        951.0
        38.0X
        94%
        83%
        LKCGP-P004801-275546-01-01-21-D1
        101.0X
        98%
        98%
        LKCGP-P004801-275546-01-01-21-D1.HW23TCCXY-L6
        878.8
        LKCGP-P004801-275546-01-01-21-D1.HW23TCCXY-L7
        934.3
        LKCGP-P004801-275546-01-01-21-D1.HW23TCCXY-L8
        826.0
        LKCGP-P005001-275776-01-03-01-R1
        99.0X
        98%
        97%
        LKCGP-P005001-275776-01-03-01-R1.HVWYTCCXY-L1
        904.2
        LKCGP-P005001-275776-01-03-01-R1.HVWYTCCXY-L2
        916.3
        LKCGP-P005001-275776-01-03-01-R1.HVWYTCCXY-L3
        918.3
        LKCGP-P005001-276091-02-03-07-G1
        926.6
        36.0X
        96%
        82%
        LKCGP-P005202-289115-01-04-01-P1
        105.0X
        98%
        98%
        LKCGP-P005202-289115-01-04-01-P1.H353NCCX2-L2
        914.0
        LKCGP-P005202-289115-01-04-01-P1.H353NCCX2-L4
        904.7
        LKCGP-P005202-289115-01-04-01-P1.H353NCCX2-L7
        970.8
        LKCGP-P005202-289117-02-04-07-G1
        928.1
        35.0X
        93%
        76%
        LKCGP-P005304-292439-02-04-07-G1
        969.9
        38.0X
        97%
        89%
        LKCGP-P005304-292442-01-04-01-R2
        111.0X
        98%
        97%
        LKCGP-P005304-292442-01-04-01-R2.H3G5KCCX2-L1
        962.5
        LKCGP-P005304-292442-01-04-01-R2.H3G5KCCX2-L2
        952.5
        LKCGP-P005304-292442-01-04-01-R2.H3G5KCCX2-L8
        990.1
        LKCGP-P005404-294240-02-06-13-P1
        92.0X
        98%
        97%
        LKCGP-P005404-294240-02-06-13-P1.H5NTWCCX2-L5
        890.9
        LKCGP-P005404-294240-02-06-13-P1.H5NTWCCX2-L6
        633.8
        LKCGP-P005404-294240-02-06-13-P1.H5NTWCCX2-L8
        950.2
        LKCGP-P005404-294497-02-06-07-G1
        937.1
        38.0X
        97%
        87%
        LKCGP-P005501-275617-05-02-08-G1
        907.8
        35.0X
        93%
        77%
        LKCGP-P005501-278087-01-02-01-D1
        91.0X
        98%
        98%
        LKCGP-P005501-278087-01-02-01-D1.HYKMGCCXY-L1
        883.3
        LKCGP-P005501-278087-01-02-01-D1.HYKMGCCXY-L2
        898.7
        LKCGP-P005501-278087-01-02-01-D1.HYKMGCCXY-L3
        910.2
        LKCGP-P005602-290690-01-01-01-R1
        113.0X
        98%
        97%
        LKCGP-P005602-290690-01-01-01-R1.H3G5KCCX2-L3
        969.3
        LKCGP-P005602-290690-01-01-01-R1.H3G5KCCX2-L4
        975.6
        LKCGP-P005602-290690-01-01-01-R1.H3G5KCCX2-L6
        981.4
        LKCGP-P005602-290694-02-01-01-G1
        983.2
        38.0X
        97%
        87%
        LKCGP-P005702-291453-02-04-07-G1
        937.8
        35.0X
        93%
        78%
        LKCGP-P005702-291574-01-04-01-D1
        92.0X
        98%
        98%
        LKCGP-P005702-291574-01-04-01-D1.H5HJVCCX2-L2
        839.8
        LKCGP-P005702-291574-01-04-01-D1.H5HJVCCX2-L4
        909.3
        LKCGP-P005702-291574-01-04-01-D1.H5HJVCCX2-L6
        974.4
        LKCGP-P005704-297004-01-04-01-R2
        105.0X
        98%
        97%
        LKCGP-P005704-297006-02-04-07-G1
        37.0X
        96%
        85%
        LKCGP-P005801-282911-01-01-01-D1
        100.0X
        98%
        97%
        LKCGP-P005801-282911-01-01-01-D1.H2VYCCCX2-L1
        889.1
        LKCGP-P005801-282911-01-01-01-D1.H2VYCCCX2-L2
        779.1
        LKCGP-P005801-282911-01-01-01-D1.H2VYCCCX2-L3
        878.2
        LKCGP-P005801-282913-02-01-07-G1
        962.1
        37.0X
        96%
        86%
        LKCGP-P005906-307371-01-04-01-D1
        93.0X
        98%
        97%
        LKCGP-P005906-307371-01-04-01-D1.H7N3CCCX2-L1
        939.7
        LKCGP-P005906-307371-01-04-01-D1.H7N3CCCX2-L2
        917.9
        LKCGP-P005906-307371-01-04-01-D1.H7N3CCCX2-L4
        934.6
        LKCGP-P005906-307590-02-04-07-G1
        877.2
        33.0X
        92%
        69%
        LKCGP-P006204-301991-02-06-07-G1
        1011.7
        38.0X
        97%
        87%
        LKCGP-P006204-301997-01-06-01-R2
        115.0X
        98%
        97%
        LKCGP-P006204-301997-01-06-01-R2.H7L5LCCX2-L5
        1021.1
        LKCGP-P006204-301997-01-06-01-R2.H7L5LCCX2-L7
        1017.0
        LKCGP-P006204-301997-01-06-01-R2.H7L5LCCX2-L8
        1011.9
        LKCGP-P006301-287949-01-04-01-P1
        98.0X
        98%
        98%
        LKCGP-P006301-287949-01-04-01-P1.H3M2GCCX2-L1
        954.1
        LKCGP-P006301-287949-01-04-01-P1.H3M2GCCX2-L2
        889.9
        LKCGP-P006301-287949-01-04-01-P1.H3M2GCCX2-L3
        957.3
        LKCGP-P006301-287951-02-04-07-G1
        946.1
        35.0X
        93%
        77%
        LKCGP-P006304-303188-01-01-01-G1
        882.9
        35.0X
        95%
        76%
        LKCGP-P006304-303189-01-01-01-D1
        103.0X
        98%
        97%
        LKCGP-P006304-303189-01-01-01-D1.H7YVYCCX2-L1
        913.2
        LKCGP-P006304-303189-01-01-01-D1.H7YVYCCX2-L4
        917.5
        LKCGP-P006304-303189-01-01-01-D1.H7YVYCCX2-L5
        920.9
        LKCGP-P006404-304450-02-02-07-G1
        894.7
        34.0X
        93%
        73%
        LKCGP-P006404-304454-01-02-01-R1
        100.0X
        98%
        98%
        LKCGP-P006404-304454-01-02-01-R1.H7N77CCX2-L5
        973.2
        LKCGP-P006404-304454-01-02-01-R1.H7N77CCX2-L6
        969.4
        LKCGP-P006404-304454-01-02-01-R1.H7N77CCX2-L8
        947.1
        LKCGP-P006501-288992-01-01-01-D1
        108.0X
        98%
        98%
        LKCGP-P006501-288992-01-01-01-D1.H33M5CCX2-L6
        985.5
        LKCGP-P006501-288992-01-01-01-D1.H33M5CCX2-L7
        971.4
        LKCGP-P006501-288992-01-01-01-D1.H33M5CCX2-L8
        937.5
        LKCGP-P006501-289018-02-01-07-G1
        954.3
        36.0X
        94%
        80%
        LKCGP-P006502-300356-02-03-03-G1
        931.8
        37.0X
        94%
        82%
        LKCGP-P006502-300779-01-03-01-P1
        106.0X
        98%
        98%
        LKCGP-P006502-300779-01-03-01-P1.H7N7YCCX2-L1
        939.8
        LKCGP-P006502-300779-01-03-01-P1.H7N7YCCX2-L5
        968.8
        LKCGP-P006502-300779-01-03-01-P1.H7N7YCCX2-L6
        971.4
        LKCGP-P006904-307586-02-01-07-G1
        918.8
        32.0X
        95%
        67%
        LKCGP-P006904-307596-01-01-01-D1
        103.0X
        98%
        97%
        LKCGP-P006904-307596-01-01-01-D1.H7NF7CCX2-L1
        936.5
        LKCGP-P006904-307596-01-01-01-D1.H7NF7CCX2-L2
        924.3
        LKCGP-P006904-307596-01-01-01-D1.H7NF7CCX2-L4
        927.4
        LKCGP-P007104-309549-01-02-05-G1
        930.2
        34.0X
        96%
        75%
        LKCGP-P007104-309550-01-02-05-R1
        107.0X
        98%
        97%
        LKCGP-P007104-309550-01-02-05-R1.HCHWGCCX2-L6
        929.5
        LKCGP-P007104-309550-01-02-05-R1.HCHWGCCX2-L7
        932.8
        LKCGP-P007104-309550-01-02-05-R1.HCHWGCCX2-L8
        929.1
        LKCP-T000101-030303-01-04-01-D1
        71.0X
        94%
        91%
        LKCP-T000101-030303-01-04-01-D1.HHGC7CCXX-L1
        861.0
        LKCP-T000101-030303-01-04-01-D1.HHGC7CCXX-L2
        893.5
        LKCP-T000101-030907-01-04-09-G1
        914.5
        37.0X
        87%
        73%
        LKCP-T000601-028528-01-01-01-R1
        75.0X
        91%
        89%
        LKCP-T000601-028528-01-01-01-R1.HHGC7CCXX-L4
        837.9
        LKCP-T000601-028528-01-01-01-R1.HHGC7CCXX-L5
        902.3
        LKCP-T000601-030378-01-01-07-G1
        962.9
        42.0X
        88%
        81%
        LKCP-T000801-030437-01-01-01-D1
        59.0X
        97%
        93%
        LKCP-T000801-030437-01-01-01-D1.HHT5TCCXX-L8
        693.3
        LKCP-T000801-030437-01-01-01-D1.HKJCTCCXX-L8
        873.8
        LKCP-T000801-030448-01-01-09-G1
        905.3
        37.0X
        86%
        72%
        LKCP-T000901-030488-01-05-09-G1
        853.9
        33.0X
        89%
        68%
        LKCP-T000901-030528-01-05-01-D1
        58.0X
        94%
        90%
        LKCP-T000901-030528-01-05-01-D1.HKJCTCCXX-L2
        832.3
        LKCP-T000901-030528-01-05-01-D1.HKJCTCCXX-L3
        843.8
        LKCP-T001101-030632-01-06-01-D1
        69.0X
        95%
        93%
        LKCP-T001101-030632-01-06-01-D1.HK7HLCCXX-L1
        937.9
        LKCP-T001101-030632-01-06-01-D1.HK7HLCCXX-L2
        929.8
        LKCP-T001101-030698-01-06-07-G1
        809.6
        28.0X
        82%
        43%
        P000806.D1vsG1
        99%
        386 bp

        Picard

        Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

        Alignment Summary

        Please note that Picard's read counts are divided by two for paired-end data.

        loading..

        Base Distribution

        Plot shows the distribution of bases by cycle.

        loading..

        GC Coverage Bias

        This plot shows bias in coverage across regions of the genome with varying GC content. A perfect library would be a flat line at y = 1.

        loading..

        Insert Size

        Plot shows the number of reads at a given insert size. Reads with different orientations are summed.

        loading..

        WGS Coverage

        The number of bases in the genome territory for each fold coverage. Note that final 1% of data is hidden to prevent very long tails.

        loading..

        WGS Filtered Bases

        For more information about the filtered categories, see the Picard documentation.

        loading..

        Samtools

        Samtools is a suite of programs for interacting with high-throughput sequencing data.

        Samtools Flagstat

        This module parses the output from samtools flagstat. All numbers in millions.

        loading..

        XY counts

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Mapped reads per contig

        The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).